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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ) $local_species = 'cqu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ) $local_species = 'car' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ) $local_species = 'mtr' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ) $local_species = 'nnu' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ) $local_species = 'psa' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/gf_data_settings.ctp, line 37 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Elements/analysis/phylogenetics_module/parameter_selection.ctp, line 64 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933 View::_renderElement() - CORE/Cake/View/View.php, line 1224 View::element() - CORE/Cake/View/View.php, line 418 include - APP/View/Analysis/custom_tree_creation.ctp, line 27 View::_evaluate() - CORE/Cake/View/View.php, line 971 View::_render() - CORE/Cake/View/View.php, line 933
$viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ) $local_species = 'ppe' $disabled = '' $selected = '' $num_hits = (int) 0
Warning (2): count(): Parameter must be an array or an object that implements Countable [APP/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp, line 33]Code Context $disabled = (!array_key_exists($local_species,$species_gene_counts))?"disabled":""; $selected = (isset($selected_species) && array_key_exists($local_species,$selected_species))?"checked='checked'":""; $num_hits = (array_key_exists($local_species,$species_gene_counts))?count($species_gene_counts[$local_species]):0; $viewFile = '/www/bioinformatics01_ro/plaza/_dev_instances/feedback/app/View/Elements/analysis/phylogenetics_module/gf_data_settings_species_selection.ctp' $dataForView = array( 'sidebar_info' => array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ) $local_species = 'sed' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $species_info = array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ) $local_species = 'vvi' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ), 'sidebar' => 'gene_family_sidebar', 'navigation_bar_info' => array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ), 'allowed_extra_sequences_types' => array( 'aa' => 'Protein', 'dna' => 'DNA' ), 'allowed_editing_methods' => array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ), 'allowed_tree_programs' => array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ), 'allowed_msa_programs' => array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ), 'allowed_number_blasthits' => array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ), 'gf_genes' => array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ), 'gf_id' => 'HOM05D001375', 'gf_types_information' => array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ), 'gf_types_configuration' => array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ), 'all_species' => array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ), 'allow_async_use' => true, 'sidebar_information' => array( 'type' => 'gf', 'id' => 'HOM05D001375' ), 'data_identifier' => 'HOM05D001375', 'data_type' => 'gf_id' ) $sidebar_info = array( 'gf_id' => 'HOM05D001375', 'msa_exists' => array( 'full' => true, 'edited' => true ), 'tree_exists' => true, 'num_genes' => '455', 'num_species' => '90' ) $sidebar = 'gene_family_sidebar' $navigation_bar_info = array( 'num_colinearity_runs' => (int) 1, 'num_colinearity_with_dating_runs' => (int) 0, 'num_functional_clusters_runs' => (int) 6, 'has_pan_genomes' => false ) $allowed_extra_sequences_types = array( 'aa' => 'Protein', 'dna' => 'DNA' ) $allowed_editing_methods = array( 'column' => 'Positions only', 'row' => 'Genes only', 'column_row' => 'Positions and Genes', 'none' => 'No editing' ) $allowed_tree_programs = array( 'fasttree' => 'FastTree', 'iqtree' => 'IQ-TREE (includes model testing)', 'raxml' => 'RAxML', 'phyml' => 'PhyML' ) $allowed_msa_programs = array( 'muscle' => 'MUSCLE', 'mafft' => 'MAFFT' ) $allowed_number_blasthits = array( (int) 0 => 'all', (int) 1 => (int) 20, (int) 2 => (int) 10, (int) 3 => (int) 5, (int) 4 => (int) 1 ) $gf_genes = array( 'A01p03630' => 'bna', 'A01p03640' => 'bna', 'A02p31290' => 'bna', 'Aa31LG2G15660' => 'aar', 'AagrBONN_evm.TU.Sc2ySwM_368.1236' => 'aag', 'AagrBONN_evm.TU.Sc2ySwM_368.1238__1239' => 'aag', 'Actinidia00601' => 'ach', 'Actinidia15940' => 'ach', 'Actinidia23682' => 'ach', 'Ah.01g022700' => 'amhyb', 'Ah.04g162350' => 'amhyb', 'Ah.06g192540' => 'amhyb', 'AL7G16330' => 'aly', 'Aqoxy3G02448' => 'aox', 'arahy.Tifrunner.gnm1.ann1.5X1F0G' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.B35Q0M' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.G2X338' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.GXD1I8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.H2TH33' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.K2FSVA' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.N2J13H' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.P8IJRR' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.R6RTRV' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.TEXQ7Y' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.UANQ1D' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.V8PLM8' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.X4TLRY' => 'arhy', 'arahy.Tifrunner.gnm1.ann1.Y5AKFB' => 'arhy', 'AT4G34880' => 'ath', 'ATR0810G032' => 'atr', 'ATR0810G034' => 'atr', 'ATR0810G043' => 'atr', 'ATR0810G054' => 'atr', 'ATR0810G069' => 'atr', 'ATR0810G070' => 'atr', 'ATR0810G087' => 'atr', 'ATR0810G091' => 'atr', 'ATR0810G111' => 'atr', 'ATR0810G116' => 'atr', 'ATR0810G121' => 'atr', 'ATR0810G142' => 'atr', 'ATR0810G156' => 'atr', 'ATR0810G157' => 'atr', 'ATR0810G162' => 'atr', 'ATR0810G163' => 'atr', 'ATR0810G168' => 'atr', 'ATR0810G172' => 'atr', 'ATR0810G180' => 'atr', 'ATR0810G186' => 'atr', 'ATR0810G195' => 'atr', 'ATR0810G207' => 'atr', 'ATR0810G216' => 'atr', 'ATR0810G229' => 'atr', 'ATR0810G230' => 'atr', 'ATR0810G259' => 'atr', 'ATR0810G284' => 'atr', 'Atru.chr5.3247' => 'acertr', 'Atru.chr5.3248' => 'acertr', 'AUR62000988' => 'cqu', 'AUR62000989' => 'cqu', 'AUR62000990' => 'cqu', 'AUR62004971' => 'cqu', 'AUR62004972' => 'cqu', 'AUR62010079' => 'cqu', 'AUR62013073' => 'cqu', 'BcaC03g16959' => 'bca', 'BcaNung00648' => 'bca', 'BolC1t00385H' => 'bol', 'BolC2t10958H' => 'bol', 'BraA01t00349Z' => 'bra', 'BraA02t08133Z' => 'bra', 'C01p03920' => 'bna', 'C02p48660' => 'bna', 'CAN.G439.21' => 'can', 'CAN.G439.22' => 'can', 'CAN.G439.23' => 'can', 'CAN.G439.24' => 'can', 'CAN.G439.25' => 'can', 'CAN.G588.33' => 'can', 'CAN.G588.35' => 'can', 'CANSAT25G0507' => 'cansat', 'CANSAT25G3585' => 'cansat', 'CARHR004760' => 'chi', 'Carub.0007s0541' => 'cru', 'Carub.0007s0542' => 'cru', 'Ca_18012_v3' => 'car', 'Ca_19038_v3' => 'car', 'Cc00_g05620' => 'ccan', 'Cc00_g05630' => 'ccan', 'Cc00_g05640' => 'ccan', 'Cc00_g05660' => 'ccan', 'Cc00_g05670' => 'ccan', 'Cc00_g05680' => 'ccan', 'Cc00_g05690' => 'ccan', 'Cc00_g16660' => 'ccan', 'Cc00_g26370' => 'ccan', 'Cc00_g34260' => 'ccan', 'Cc00_g35910' => 'ccan', 'Cc02_g14740' => 'ccan', 'Cc02_g16440' => 'ccan', 'Cc02_g29320' => 'ccan', 'Cc02_g29340' => 'ccan', 'Cfa005192' => 'cfa', 'Cfa005193' => 'cfa', 'Cfa005194' => 'cfa', 'Cfa005195' => 'cfa', 'Cfa005196' => 'cfa', 'Cfa005197' => 'cfa', 'Cfa005200' => 'cfa', 'Cfa005201' => 'cfa', 'Cfa005202' => 'cfa', 'Cfa005204' => 'cfa', 'Cfa005205' => 'cfa', 'Cfa005206' => 'cfa', 'Cfa005207' => 'cfa', 'Cfa024229' => 'cfa', 'Cfa025084' => 'cfa', 'Ciclev10028187m.g' => 'ccl', 'Ciclev10028203m.g' => 'ccl', 'Ciclev10028286m.g' => 'ccl', 'Ciclev10030231m.g' => 'ccl', 'Ciclev10030294m.g' => 'ccl', 'CiPaw.05G078000' => 'cil', 'CiPaw.05G078100' => 'cil', 'CiPaw.05G078200' => 'cil', 'CiPaw.05G078300' => 'cil', 'CiPaw.05G078400' => 'cil', 'CiPaw.05G078500' => 'cil', 'CiPaw.05G078600' => 'cil', 'CiPaw.06G124600' => 'cil', 'CiPaw.06G124700' => 'cil', 'ClCG02G004250' => 'cla', 'ClCG02G004260' => 'cla', 'ClCG02G011630' => 'cla', 'COL.COLO4_17267' => 'col', 'COL.COLO4_17268' => 'col', 'COL.COLO4_17269' => 'col', 'COL.COLO4_20157' => 'col', 'Cpa.g.sc37.180' => 'cpa', 'Cpa.g.sc37.181' => 'cpa', 'CsaV3_2G015790' => 'csa', 'CsaV3_2G015800' => 'csa', 'CsaV3_2G015820' => 'csa', 'CsaV3_7G000850' => 'csa', 'CsaV3_7G000860' => 'csa', 'CSS0001184' => 'camsi', 'CSS0004892' => 'camsi', 'CSS0009738' => 'camsi', 'CSS0010198' => 'camsi', 'CSS0013885' => 'camsi', 'CSS0022355' => 'camsi', 'CSS0022671' => 'camsi', 'CSS0024867' => 'camsi', 'CSS0035205' => 'camsi', 'CSS0036625' => 'camsi', 'CSS0048263' => 'camsi', 'DCAR_003244' => 'dca', 'DCAR_003706' => 'dca', 'DCAR_003708' => 'dca', 'DCAR_005955' => 'dca', 'Dinv04961' => 'din', 'Dinv04962' => 'din', 'Dinv07082' => 'din', 'Dinv39525' => 'din', 'Dinv41966' => 'din', 'Dinv41969' => 'din', 'Dinv42666' => 'din', 'Duzib052G0515' => 'dzi', 'Duzib132G1101' => 'dzi', 'ECA233G0605' => 'eca', 'ECA246G1973' => 'eca', 'EL10Ac4g09167' => 'bvu', 'EL10Ac9g21426' => 'bvu', 'Eucgr.G01762' => 'egr', 'Eucgr.G01763' => 'egr', 'Eucgr.I01380' => 'egr', 'Eucgr.I01381' => 'egr', 'Eucgr.I01382' => 'egr', 'Eucgr.I01383' => 'egr', 'Eucgr.I01384' => 'egr', 'Eucgr.I01385' => 'egr', 'Eucgr.I01386' => 'egr', 'Eucgr.I01387' => 'egr', 'Eucgr.I01388' => 'egr', 'Eucgr.I01389' => 'egr', 'Eucgr.L03196' => 'egr', 'Eucgr.L03443' => 'egr', 'FAN15G0808' => 'fan', 'FAN15G3245' => 'fan', 'FAN20G1953' => 'fan', 'FAN20G2903' => 'fan', 'FAN24G2437' => 'fan', 'FAN27G0194' => 'fan', 'FAN27G1777' => 'fan', 'FvH4_2g01710' => 'fve', 'FvH4_2g01720' => 'fve', 'FvH4_2g01722' => 'fve', 'FvH4_2g01800' => 'fve', 'Glyma.05G149500' => 'gma', 'Glyma.08G106000' => 'gma', 'Glyma.08G106100' => 'gma', 'Glyma.08G106200' => 'gma', 'Gohir.A01G164350' => 'ghi', 'Gohir.A01G164400' => 'ghi', 'Gohir.D01G156300' => 'ghi', 'Gohir.D01G156400' => 'ghi', 'Gorai.002G193800' => 'gra', 'Gorai.002G193900' => 'gra', 'Gorai.002G194000' => 'gra', 'GSVIVG01024064001' => 'vvi', 'GSVIVG01024065001' => 'vvi', 'GSVIVG01024066001' => 'vvi', 'GSVIVG01024067001' => 'vvi', 'GSVIVG01024068001' => 'vvi', 'GSVIVG01024069001' => 'vvi', 'GSVIVG01024070001' => 'vvi', 'HanXRQChr15g0472011' => 'han', 'HanXRQChr15g0472021' => 'han', 'Haze_02187' => 'cav', 'Haze_10411' => 'cav', 'Haze_10412' => 'cav', 'Haze_13060' => 'cav', 'Haze_27213' => 'cav', 'Hma1.2p1_0023F.1_g015520' => 'hma', 'HPP92_004986' => 'vpl', 'HPP92_004987' => 'vpl', 'HPP92_004989' => 'vpl', 'HPP92_008450' => 'vpl', 'HPP92_025555' => 'vpl', 'HPP92_027497' => 'vpl', 'HPP92_027498' => 'vpl', 'Hund06412' => 'sun', 'Lalb_Chr03g0025011' => 'lal', 'Lalb_Chr12g0205951' => 'lal', 'Lj3g0000984' => 'lja', 'Lj3g0011878' => 'lja', 'Lj4g0007390' => 'lja', 'Lj5A183G94' => 'lonja', 'Lj5A183T92' => 'lonja', 'Lj5C183G12' => 'lonja', 'Lj6g0008557' => 'lja', 'Lsat_1_v5_gn_2_119161' => 'lsa', 'Lsat_1_v5_gn_3_45780' => 'lsa', 'Lsat_1_v5_gn_3_45801' => 'lsa', 'Lsat_1_v5_gn_3_45840' => 'lsa', 'Lsat_1_v5_gn_8_126020' => 'lsa', 'Manes.04G077700' => 'mes', 'Manes.04G077750' => 'mes', 'Manes.11G090900' => 'mes', 'Manes.11G091058' => 'mes', 'Manes.11G091532' => 'mes', 'MBI09_g15952_MAGBIO' => 'mbi', 'MBI09_g15954_MAGBIO' => 'mbi', 'MD05G1117000' => 'mdo', 'MD05G1117200' => 'mdo', 'MD10G1120200' => 'mdo', 'MD10G1120300' => 'mdo', 'MD10G1120400' => 'mdo', 'MD10G1120600' => 'mdo', 'Medtr4g073970' => 'mtr', 'Medtr4g073980' => 'mtr', 'Medtr4g074030' => 'mtr', 'Medtr8g080840' => 'mtr', 'Medtr8g080850' => 'mtr', 'Medtr8g080870' => 'mtr', 'Medtr8g080880' => 'mtr', 'Medtr8g080890' => 'mtr', 'Medtr8g097220' => 'mtr', 'MELO3C013371.2' => 'cme', 'MELO3C013372.2' => 'cme', 'MELO3C020792.2' => 'cme', 'MELO3C020793.2' => 'cme', 'MELO3C020794.2' => 'cme', 'Migut.B00113' => 'egut', 'Migut.B00114' => 'egut', 'MSTRG.16887' => 'ama', 'Nitab4.5_0000283g0050' => 'nta', 'Nitab4.5_0000615g0030' => 'nta', 'Nitab4.5_0000615g0050' => 'nta', 'Nitab4.5_0000980g0060' => 'nta', 'Nitab4.5_0003269g0060' => 'nta', 'Nitab4.5_0004220g0010' => 'nta', 'Nitab4.5_0005222g0010' => 'nta', 'Nn1g05916' => 'nnu', 'Nn2g14360' => 'nnu', 'Nn6g35725' => 'nnu', 'Nn7g36788' => 'nnu', 'Oeu047784.1' => 'oeu', 'Oeu047785.1' => 'oeu', 'Oeu060422.1' => 'oeu', 'Os01g0115200' => 'osa', 'Os04g0182875' => 'osa', 'Os04g0182900' => 'osa', 'Os04g0183300' => 'osa', 'Os04g0183500' => 'osa', 'Os04g0184100' => 'osa', 'Os04g0184500' => 'osa', 'Os04g0184801' => 'osa', 'Os04g0185000' => 'osa', 'Os06g0271300' => 'osa', 'Os10g0155400' => 'osa', 'Os11g0123033' => 'osa', 'Peaxi162Scf00217g00621' => 'pax', 'Peaxi162Scf00362g00956' => 'pax', 'Peaxi162Scf00362g00957' => 'pax', 'Peaxi162Scf00684g00028' => 'pax', 'Peaxi162Scf00684g00029' => 'pax', 'PGR042G2671' => 'pgr', 'PGR142G1342' => 'pgr', 'PGR142G3522' => 'pgr', 'PGSC0003DMG400001625' => 'stu', 'PGSC0003DMG400001626' => 'stu', 'PGSC0003DMG400002019' => 'stu', 'PGSC0003DMG400018706' => 'stu', 'Phvul.L003946' => 'pvu', 'Potri.004G169300' => 'ptr', 'Potri.004G169400' => 'ptr', 'Potri.004G171000' => 'ptr', 'Potri.004G171300' => 'ptr', 'Potri.009G130400' => 'ptr', 'Potri.009G130500' => 'ptr', 'Potri.009G130700' => 'ptr', 'Prupe.8G161600' => 'ppe', 'Prupe.8G161700' => 'ppe', 'Prupe.8G161800' => 'ppe', 'Prupe.8G161900' => 'ppe', 'Psat1g115200' => 'psa', 'Psat2g068120' => 'psa', 'Psat7g075560' => 'psa', 'Psat7g174360' => 'psa', 'Psat7g174400' => 'psa', 'PSO135G0202' => 'pso', 'PSO135G0216' => 'pso', 'PSO135G0393' => 'pso', 'PSO210G1458' => 'pso', 'PSO210G2448' => 'pso', 'PSO210G4012' => 'pso', 'PSO210G5656' => 'pso', 'PSO210G7078' => 'pso', 'PSO386G0109' => 'pso', 'PSO675G3189' => 'pso', 'PSO700G0144' => 'pso', 'PSO724G0384' => 'pso', 'PSO724G0677' => 'pso', 'QL02p039765' => 'qlo', 'QL11p047888' => 'qlo', 'QL11p047895' => 'qlo', 'QL11p047901' => 'qlo', 'QL11p047948' => 'qlo', 'QL11p047952' => 'qlo', 'QL11p047962' => 'qlo', 'QL11p048011' => 'qlo', 'QL11p048018' => 'qlo', 'QL11p048023' => 'qlo', 'QL11p048064' => 'qlo', 'QL11p048093' => 'qlo', 'QL11p048119' => 'qlo', 'QL11p048341' => 'qlo', 'QL11p048406' => 'qlo', 'QL11p048533' => 'qlo', 'QL11p048537' => 'qlo', 'QL11p049019' => 'qlo', 'QL11p049120' => 'qlo', 'QL11p049125' => 'qlo', 'RcHm_v2.0_Chr6g0244611' => 'rch', 'RcHm_v2.0_Chr6g0244621' => 'rch', 'RcHm_v2.0_Chr6g0244631' => 'rch', 'RcHm_v2.0_Chr6g0244661' => 'rch', 'RcHm_v2.0_Chr6g0244671' => 'rch', 'RcHm_v2.0_Chr6g0244701' => 'rch', 'RcHm_v2.0_Chr6g0244721' => 'rch', 'RcHm_v2.0_Chr6g0244741' => 'rch', 'RcHm_v2.0_Chr6g0244751' => 'rch', 'Rhsim05G0062500' => 'rsi', 'Rhsim05G0062700' => 'rsi', 'Rhsim08G0183700' => 'rsi', 'Rhsim11G0189200' => 'rsi', 'Sabra04G0113500' => 'sbr', 'Sabra04G0113700' => 'sbr', 'Sabra04G0113900' => 'sbr', 'Sabra09G0101000' => 'sbr', 'SalBow6G2456' => 'sbo', 'SalBow6G5025' => 'sbo', 'Sc08g0003130' => 'sci', 'Sc08g0003140' => 'sci', 'Sc14g0002140' => 'sci', 'Sc14g0002150' => 'sci', 'Sc14g0002160' => 'sci', 'Sc14g0002170' => 'sci', 'Sc18g0006620' => 'sci', 'Sed0008875' => 'sed', 'Sed0012086' => 'sed', 'Sed0022074' => 'sed', 'Sed0027530' => 'sed', 'SEGI_03091' => 'sgi', 'SEGI_05343' => 'sgi', 'SEGI_09884' => 'sgi', 'SEGI_11928' => 'sgi', 'SEGI_12574' => 'sgi', 'SEGI_26009' => 'sgi', 'SEGI_26808' => 'sgi', 'SEGI_28744' => 'sgi', 'SEGI_28756' => 'sgi', 'SEGI_29159' => 'sgi', 'SEGI_34004' => 'sgi', 'SEGI_34389' => 'sgi', 'SEGI_35733' => 'sgi', 'SEGI_40412' => 'sgi', 'SGA_v2.0_scaffold58G20422' => 'sas', 'SGA_v2.0_scaffold58G20423' => 'sas', 'SMO134G0263' => 'smo', 'SMO137G0127' => 'smo', 'SMO271G0054' => 'smo', 'Solyc01g111210.3' => 'sly', 'Solyc01g111220.3' => 'sly', 'Solyc11g071550.2' => 'sly', 'Sopen01g053270' => 'spe', 'Sopen01g053280' => 'spe', 'Sopen11g029240' => 'spe', 'TAR375G0188' => 'tar', 'TAR381G0102' => 'tar', 'TAR381G0790' => 'tar', 'TAR381G0991' => 'tar', 'TAR381G1031' => 'tar', 'TAR381G1166' => 'tar', 'TAR381G1406' => 'tar', 'TAR628G0562' => 'tar', 'TAR628G1148' => 'tar', 'TAR628G1402' => 'tar', 'THA.LOC104804337' => 'tha', 'Thecc.02G065900' => 'tca', 'Thecc.02G066000' => 'tca', 'Thecc.02G066100' => 'tca', 'Thecc.05G242200' => 'tca', 'Thhalv10025156m.g' => 'esa', 'TPR.G11956' => 'tpr', 'TPR.G13221' => 'tpr', 'TPR.G19897' => 'tpr', 'TPR.G26564' => 'tpr', 'TPR.G26565' => 'tpr', 'TPR.G26569' => 'tpr', 'TPR.G39404' => 'tpr', 'TWI75G0690' => 'twi', 'TWI75G1237' => 'twi', 'TWI75G1622' => 'twi', 'TWI75G1826' => 'twi', 'unitig_21.g20823' => 'ugi', 'unitig_21.g20829' => 'ugi', 'vmacro02256' => 'vma', 'vmacro17371' => 'vma', 'vmacro17372' => 'vma', 'vmacro17375' => 'vma', 'vmacro19250' => 'vma', 'Zm00001eb087630' => 'zma', 'Zm00001eb321360' => 'zma' ) $gf_id = 'HOM05D001375' $gf_types_information = array( 'HOMFAM' => array( 'id' => 'HOMFAM', 'name' => 'Homologous gene family', 'gene_type' => 'coding', 'parent_id' => '', 'ancestry' => 'homology' ), 'ORTHOFAM' => array( 'id' => 'ORTHOFAM', 'name' => 'Orthologous gene family', 'gene_type' => 'coding', 'parent_id' => 'HOMFAM', 'ancestry' => 'orthology' ) ) $gf_types_configuration = array( 'HOMFAM' => array( 'order' => '1', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ), 'ORTHOFAM' => array( 'order' => '2', 'show_parentless_subfamilies' => 'false', 'show_table' => 'true', 'show_orphan' => false ) ) $all_species = array( 'acertr' => array( 'species' => 'acertr', 'common_name' => 'Acer truncatum', 'tax_id' => '47965', 'version' => 'v2.0' ), 'ach' => array( 'species' => 'ach', 'common_name' => 'Actinidia chinensis', 'tax_id' => '3625', 'version' => 'V3.0' ), 'aar' => array( 'species' => 'aar', 'common_name' => 'Aethionema arabicum', 'tax_id' => '228871', 'version' => 'v3.1' ), 'amhyb' => array( 'species' => 'amhyb', 'common_name' => 'Amaranthus hybridus', 'tax_id' => '3565', 'version' => 'v1.0' ), 'atr' => array( 'species' => 'atr', 'common_name' => 'Amborella trichopoda', 'tax_id' => '13333', 'version' => 'JGI v1.0' ), 'aag' => array( 'species' => 'aag', 'common_name' => 'Anthoceros agrestis', 'tax_id' => '41834', 'version' => 'v1.1' ), 'aox' => array( 'species' => 'aox', 'common_name' => 'Aquilegia oxysepala', 'tax_id' => '432649', 'version' => 'v1.0' ), 'aly' => array( 'species' => 'aly', 'common_name' => 'Arabidopsis lyrata', 'tax_id' => '59689', 'version' => 'JGI v2.1' ), 'ath' => array( 'species' => 'ath', 'common_name' => 'Arabidopsis thaliana', 'tax_id' => '3702', 'version' => 'Araport11' ), 'arhy' => array( 'species' => 'arhy', 'common_name' => 'Arachis hypogaea', 'tax_id' => '3818', 'version' => 'v1.0' ), 'ama' => array( 'species' => 'ama', 'common_name' => 'Avicennia marina', 'tax_id' => '82927', 'version' => 'v1.1 20200527' ), 'bvu' => array( 'species' => 'bvu', 'common_name' => 'Beta vulgaris', 'tax_id' => '161934', 'version' => 'EL10_1.0' ), 'bca' => array( 'species' => 'bca', 'common_name' => 'Brassica carinata', 'tax_id' => '52824', 'version' => 'V1.0' ), 'bna' => array( 'species' => 'bna', 'common_name' => 'Brassica napus', 'tax_id' => '3708', 'version' => 'v2.0' ), 'bol' => array( 'species' => 'bol', 'common_name' => 'Brassica oleracea', 'tax_id' => '109376', 'version' => 'v1.0' ), 'bra' => array( 'species' => 'bra', 'common_name' => 'Brassica rapa', 'tax_id' => '3711', 'version' => 'v1.0' ), 'camsi' => array( 'species' => 'camsi', 'common_name' => 'Camellia sinensis var. sinensis', 'tax_id' => '542762', 'version' => 'CSS_ChrLev_20200506' ), 'cansat' => array( 'species' => 'cansat', 'common_name' => 'Cannabis sativa', 'tax_id' => '3483', 'version' => 'cs10' ), 'cru' => array( 'species' => 'cru', 'common_name' => 'Capsella rubella', 'tax_id' => '81985', 'version' => 'JGI v1.1' ), 'can' => array( 'species' => 'can', 'common_name' => 'Capsicum annuum', 'tax_id' => '4072', 'version' => 'Pepper Genome v2.0' ), 'chi' => array( 'species' => 'chi', 'common_name' => 'Cardamine hirsuta', 'tax_id' => '50463', 'version' => 'v1.0' ), 'cpa' => array( 'species' => 'cpa', 'common_name' => 'Carica papaya', 'tax_id' => '3649', 'version' => 'JGI ASGPB0.4' ), 'cfa' => array( 'species' => 'cfa', 'common_name' => 'Carpinus fangiana', 'tax_id' => '176857', 'version' => 'v1.0' ), 'cil' => array( 'species' => 'cil', 'common_name' => 'Carya illinoinensis', 'tax_id' => '32201', 'version' => 'v1.1' ), 'cde' => array( 'species' => 'cde', 'common_name' => 'Ceratophyllum demersum', 'tax_id' => '4428', 'version' => 'v1.0' ), 'cbr' => array( 'species' => 'cbr', 'common_name' => 'Chara braunii', 'tax_id' => '69332', 'version' => 'Cbr1.0' ), 'cqu' => array( 'species' => 'cqu', 'common_name' => 'Chenopodium quinoa', 'tax_id' => '63459', 'version' => 'KAUST v1.0' ), 'cre' => array( 'species' => 'cre', 'common_name' => 'Chlamydomonas reinhardtii', 'tax_id' => '3055', 'version' => 'JGI v5.5' ), 'car' => array( 'species' => 'car', 'common_name' => 'Cicer arietinum L.', 'tax_id' => '3827', 'version' => 'v3.0' ), 'cla' => array( 'species' => 'cla', 'common_name' => 'Citrullus lanatus', 'tax_id' => '3654', 'version' => 'WCG v2.0' ), 'ccl' => array( 'species' => 'ccl', 'common_name' => 'Citrus clementina', 'tax_id' => '85681', 'version' => 'JGI v1.0' ), 'ccan' => array( 'species' => 'ccan', 'common_name' => 'Coffea canephora', 'tax_id' => '49390', 'version' => 'Coffee Genome Hub v1' ), 'col' => array( 'species' => 'col', 'common_name' => 'Corchorus olitorius', 'tax_id' => '93759', 'version' => 'GenBank v1.0' ), 'cav' => array( 'species' => 'cav', 'common_name' => 'Corylus avellana', 'tax_id' => '13451', 'version' => 'v1.0' ), 'cme' => array( 'species' => 'cme', 'common_name' => 'Cucumis melo', 'tax_id' => '3656', 'version' => 'Melonomics v3.6.1' ), 'csa' => array( 'species' => 'csa', 'common_name' => 'Cucumis sativus L.', 'tax_id' => '3659', 'version' => 'v3.0' ), 'dca' => array( 'species' => 'dca', 'common_name' => 'Daucus carota', 'tax_id' => '4039', 'version' => 'JGI v2.0' ), 'din' => array( 'species' => 'din', 'common_name' => 'Davidia involucrata', 'tax_id' => '16924', 'version' => 'v1.0' ), 'dzi' => array( 'species' => 'dzi', 'common_name' => 'Durio zibethinus', 'tax_id' => '66656', 'version' => 'Duzib1.0' ), 'eca' => array( 'species' => 'eca', 'common_name' => 'Erigeron canadensis', 'tax_id' => '72917', 'version' => 'V1.0' ), 'egut' => array( 'species' => 'egut', 'common_name' => 'Erythranthe guttata', 'tax_id' => '4155', 'version' => 'v2.0' ), 'egr' => array( 'species' => 'egr', 'common_name' => 'Eucalyptus grandis', 'tax_id' => '71139', 'version' => 'v2.0' ), 'esa' => array( 'species' => 'esa', 'common_name' => 'Eutrema salsugineum', 'tax_id' => '72664', 'version' => 'v1.0' ), 'fve' => array( 'species' => 'fve', 'common_name' => 'Fragaria vesca', 'tax_id' => '57918', 'version' => 'V4.0.a2' ), 'fan' => array( 'species' => 'fan', 'common_name' => 'Fragaria x ananassa', 'tax_id' => '3747', 'version' => 'V1.0.a1' ), 'gma' => array( 'species' => 'gma', 'common_name' => 'Glycine max', 'tax_id' => '3847', 'version' => 'JGI Wm82.a4.v1' ), 'ghi' => array( 'species' => 'ghi', 'common_name' => 'Gossypium hirsutum', 'tax_id' => '3635', 'version' => 'v2.1' ), 'gra' => array( 'species' => 'gra', 'common_name' => 'Gossypium raimondii', 'tax_id' => '29730', 'version' => 'v2.1' ), 'han' => array( 'species' => 'han', 'common_name' => 'Helianthus annuus', 'tax_id' => '4232', 'version' => 'r1.2' ), 'hma' => array( 'species' => 'hma', 'common_name' => 'Hydrangea macrophylla', 'tax_id' => '23110', 'version' => 'v2.1' ), 'lsa' => array( 'species' => 'lsa', 'common_name' => 'Lactuca sativa', 'tax_id' => '4236', 'version' => 'v8.0' ), 'lonja' => array( 'species' => 'lonja', 'common_name' => 'Lonicera japonica', 'tax_id' => '105884', 'version' => 'v1.0' ), 'lja' => array( 'species' => 'lja', 'common_name' => 'Lotus japonicus', 'tax_id' => '34305', 'version' => 'Lj1.0v1' ), 'lal' => array( 'species' => 'lal', 'common_name' => 'Lupinus albus', 'tax_id' => '3870', 'version' => 'v1.0' ), 'mbi' => array( 'species' => 'mbi', 'common_name' => 'Magnolia biondii', 'tax_id' => '86725', 'version' => 'v1.0' ), 'mdo' => array( 'species' => 'mdo', 'common_name' => 'Malus domestica', 'tax_id' => '3750', 'version' => 'GDDH13 v1.1' ), 'mes' => array( 'species' => 'mes', 'common_name' => 'Manihot esculenta', 'tax_id' => '3983', 'version' => 'v8.1' ), 'mpo' => array( 'species' => 'mpo', 'common_name' => 'Marchantia polymorpha', 'tax_id' => '3197', 'version' => 'JGI v3.1' ), 'mtr' => array( 'species' => 'mtr', 'common_name' => 'Medicago truncatula', 'tax_id' => '3880', 'version' => 'JGI Mt4.0v1' ), 'mco' => array( 'species' => 'mco', 'common_name' => 'Micromonas commoda', 'tax_id' => '296587', 'version' => 'JGI v3.0' ), 'nnu' => array( 'species' => 'nnu', 'common_name' => 'Nelumbo nucifera', 'tax_id' => '4432', 'version' => 'v2.0' ), 'nta' => array( 'species' => 'nta', 'common_name' => 'Nicotiana tabacum', 'tax_id' => '4097', 'version' => 'Edwards2017' ), 'oeu' => array( 'species' => 'oeu', 'common_name' => 'Olea europaea', 'tax_id' => '4146', 'version' => 'v1.0' ), 'osa' => array( 'species' => 'osa', 'common_name' => 'Oryza sativa ssp. japonica', 'tax_id' => '39947', 'version' => 'IRGSP-1.0-2021-05-10' ), 'pso' => array( 'species' => 'pso', 'common_name' => 'Papaver somniferum', 'tax_id' => '3469', 'version' => 'ASM357369v1' ), 'pax' => array( 'species' => 'pax', 'common_name' => 'Petunia axillaris', 'tax_id' => '33119', 'version' => 'Sol Genomics v1.6.2' ), 'pvu' => array( 'species' => 'pvu', 'common_name' => 'Phaseolus vulgaris', 'tax_id' => '3885', 'version' => 'v2.1' ), 'ppa' => array( 'species' => 'ppa', 'common_name' => 'Physcomitrium patens', 'tax_id' => '3218', 'version' => 'JGI v3.3' ), 'psa' => array( 'species' => 'psa', 'common_name' => 'Pisum sativum', 'tax_id' => '3888', 'version' => 'V1.0a' ), 'ptr' => array( 'species' => 'ptr', 'common_name' => 'Populus trichocarpa', 'tax_id' => '3694', 'version' => 'JGI v4.1' ), 'pco' => array( 'species' => 'pco', 'common_name' => 'Prasinoderma coloniale', 'tax_id' => '156133', 'version' => 'v1.0' ), 'ppe' => array( 'species' => 'ppe', 'common_name' => 'Prunus persica', 'tax_id' => '3760', 'version' => 'v2.1' ), 'pgr' => array( 'species' => 'pgr', 'common_name' => 'Punica granatum', 'tax_id' => '22663', 'version' => 'ASM765513v2' ), 'qlo' => array( 'species' => 'qlo', 'common_name' => 'Quercus lobata', 'tax_id' => '97700', 'version' => 'v3.0' ), 'rsi' => array( 'species' => 'rsi', 'common_name' => 'Rhododendron simsii', 'tax_id' => '118357', 'version' => 'v1.0' ), 'rch' => array( 'species' => 'rch', 'common_name' => 'Rosa chinensis', 'tax_id' => '74649', 'version' => 'v2.0' ), 'sbr' => array( 'species' => 'sbr', 'common_name' => 'Salix brachista', 'tax_id' => '2182728', 'version' => 'v1.0' ), 'sbo' => array( 'species' => 'sbo', 'common_name' => 'Salvia bowleyana', 'tax_id' => '424416', 'version' => 'v1.0' ), 'shi' => array( 'species' => 'shi', 'common_name' => 'Sapria himalayana', 'tax_id' => '289637', 'version' => 'v1.0' ), 'spa' => array( 'species' => 'spa', 'common_name' => 'Schrenkiella parvula', 'tax_id' => '98039', 'version' => 'v2.2' ), 'sed' => array( 'species' => 'sed', 'common_name' => 'Sechium edule', 'tax_id' => '184140', 'version' => 'v1.0' ), 'smo' => array( 'species' => 'smo', 'common_name' => 'Selaginella moellendorffii', 'tax_id' => '88036', 'version' => 'v1.0' ), 'sun' => array( 'species' => 'sun', 'common_name' => 'Selenicereus undatus', 'tax_id' => '176265', 'version' => 'v1.0' ), 'sgi' => array( 'species' => 'sgi', 'common_name' => 'Sequoiadendron giganteum', 'tax_id' => '99814', 'version' => 'V2.0' ), 'sci' => array( 'species' => 'sci', 'common_name' => 'Simmondsia chinensis', 'tax_id' => '3999', 'version' => 'sc1' ), 'sly' => array( 'species' => 'sly', 'common_name' => 'Solanum lycopersicum', 'tax_id' => '4081', 'version' => 'ITAG4.0' ), 'spe' => array( 'species' => 'spe', 'common_name' => 'Solanum pennellii', 'tax_id' => '28526', 'version' => 'V2.0' ), 'stu' => array( 'species' => 'stu', 'common_name' => 'Solanum tuberosum', 'tax_id' => '4113', 'version' => 'JGI v4.03' ), 'sas' => array( 'species' => 'sas', 'common_name' => 'Striga asiatica', 'tax_id' => '4170', 'version' => 'v2.02' ), 'tha' => array( 'species' => 'tha', 'common_name' => 'Tarenaya hassleriana', 'tax_id' => '28532', 'version' => 'RefSeq v1' ), 'tca' => array( 'species' => 'tca', 'common_name' => 'Theobroma cacao', 'tax_id' => '3641', 'version' => 'V2.1' ), 'tpr' => array( 'species' => 'tpr', 'common_name' => 'Trifolium pratense', 'tax_id' => '57577', 'version' => 'V2.0' ), 'twi' => array( 'species' => 'twi', 'common_name' => 'Tripterygium wilfordii', 'tax_id' => '458696', 'version' => 'ASM1340144v1' ), 'tar' => array( 'species' => 'tar', 'common_name' => 'Trochodendron aralioides', 'tax_id' => '4407', 'version' => 'v1.0' ), 'ugi' => array( 'species' => 'ugi', 'common_name' => 'Utricularia gibba', 'tax_id' => '13748', 'version' => 'v1.1F' ), 'vma' => array( 'species' => 'vma', 'common_name' => 'Vaccinium macrocarpon', 'tax_id' => '13750', 'version' => 'V1.0' ), 'vpl' => array( 'species' => 'vpl', 'common_name' => 'Vanilla planifolia', 'tax_id' => '51239', 'version' => 'Elo Vpla-A Principal v1.0' ), 'vmu' => array( 'species' => 'vmu', 'common_name' => 'Vigna mungo', 'tax_id' => '3915', 'version' => 'ASM1342719v1' ), 'vvi' => array( 'species' => 'vvi', 'common_name' => 'Vitis vinifera', 'tax_id' => '29760', 'version' => 'Genoscope.12x' ), 'zma' => array( 'species' => 'zma', 'common_name' => 'Zea mays', 'tax_id' => '4577', 'version' => 'NAM v5.0' ) ) $allow_async_use = true $sidebar_information = array( 'type' => 'gf', 'id' => 'HOM05D001375' ) $data_identifier = 'HOM05D001375' $data_type = 'gf_id' $species_gene_counts = array( 'bna' => (int) 5, 'aar' => (int) 1, 'aag' => (int) 2, 'ach' => (int) 3, 'amhyb' => (int) 3, 'aly' => (int) 1, 'aox' => (int) 1, 'arhy' => (int) 14, 'ath' => (int) 1, 'atr' => (int) 27, 'acertr' => (int) 2, 'cqu' => (int) 7, 'bca' => (int) 2, 'bol' => (int) 2, 'bra' => (int) 2, 'can' => (int) 7, 'cansat' => (int) 2, 'chi' => (int) 1, 'cru' => (int) 2, 'car' => (int) 2, 'ccan' => (int) 15, 'cfa' => (int) 15, 'ccl' => (int) 5, 'cil' => (int) 9, 'cla' => (int) 3, 'col' => (int) 4, 'cpa' => (int) 2, 'csa' => (int) 5, 'camsi' => (int) 11, 'dca' => (int) 4, 'din' => (int) 7, 'dzi' => (int) 2, 'eca' => (int) 2, 'bvu' => (int) 2, 'egr' => (int) 14, 'fan' => (int) 7, 'fve' => (int) 4, 'gma' => (int) 4, 'ghi' => (int) 4, 'gra' => (int) 3, 'vvi' => (int) 7, 'han' => (int) 2, 'cav' => (int) 5, 'hma' => (int) 1, 'vpl' => (int) 7, 'sun' => (int) 1, 'lal' => (int) 2, 'lja' => (int) 4, 'lonja' => (int) 3, 'lsa' => (int) 5, 'mes' => (int) 5, 'mbi' => (int) 2, 'mdo' => (int) 6, 'mtr' => (int) 9, 'cme' => (int) 5, 'egut' => (int) 2, 'ama' => (int) 1, 'nta' => (int) 7, 'nnu' => (int) 4, 'oeu' => (int) 3, 'osa' => (int) 12, 'pax' => (int) 5, 'pgr' => (int) 3, 'stu' => (int) 4, 'pvu' => (int) 1, 'ptr' => (int) 7, 'ppe' => (int) 4, 'psa' => (int) 5, 'pso' => (int) 13, 'qlo' => (int) 20, 'rch' => (int) 9, 'rsi' => (int) 4, 'sbr' => (int) 4, 'sbo' => (int) 2, 'sci' => (int) 7, 'sed' => (int) 4, 'sgi' => (int) 14, 'sas' => (int) 2, 'smo' => (int) 3, 'sly' => (int) 3, 'spe' => (int) 3, 'tar' => (int) 10, 'tha' => (int) 1, 'tca' => (int) 4, 'esa' => (int) 1, 'tpr' => (int) 7, 'twi' => (int) 4, 'ugi' => (int) 2, 'vma' => (int) 5, 'zma' => (int) 2 ) $gf_gene_species = 'zma' $gf_gene_id = 'Zm00001eb321360' $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